Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

Dai, Fei; Chen, Zhong‐Hua; Wang, Xiaolei; Li, Zefeng; Jin, Gulei; Wu, Dezhi; Cai, Shengguan; Wang, Ning; Wu, Feibo; Nevo, Eviatar; Zhang, Guoping

doi:10.1073/pnas.1414335111

Cited by 74 publications

(83 citation statements)

References 54 publications

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“…Although the divergences between the Tibetan wild and cultivated barley are evident, they are even closer in comparison with barley accessions from Europe, East Asia, and Israel, which are sequenced by IBSC. This result came from analyses of PCA, STRUCTURE, F st , and cluster and is consistent with that obtained by transcriptome sequencing (12). Therefore, introducing the gene pool of Tibetan wild barley and those from non-Tibetan groups into Tibetan hulless barley may be helpful in widening the genetic background of Tibetan hulless barley.…”

Section: Discussionsupporting

confidence: 84%

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The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

Zeng

Long

Wang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.Tibetan hulless barley | Triticeae evolution | genetic diversity | adaptation | selective sweep

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Section: Discussionsupporting

confidence: 84%

“…nudum), with naked caryopsis, is mainly cultivated in Tibet and its vicinity, which is one of the domestication and diversity centers for cultivated barley (12)(13)(14)(15)(16). The adaptation to extreme environmental conditions in high altitudes made it the staple food for Tibetans beginning at least 3,500-4,000 years ago (17,18).…”

mentioning

confidence: 99%

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

Zeng

Long

Wang

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

147

131

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“…These results provided evidence that the SNP T643A might cause a loss of function of Nud and that the middle motif might be essential for function. Dai et al (2014) found that hulless barley in Tibet differed from modern cultivated barley at the genomic level and it probably existed in an early stage of domestication. Our findings in the present study provide evidence for a new origin of naked barley in Tibet and support the above viewpoint.…”

Section: Discussionmentioning

confidence: 99%

A Single Nucleotide Polymorphism of Nud Converts the Caryopsis Type of Barley (Hordeum Vulgare L.)

Long

Deng

et al. 2015

Plant Mol Biol Rep

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Whether the caryopsis of barley is naked or covered is controlled by the Nud gene encoding an ethylene response factor (ERF) family transcription factor (TF) of the AP2/ERF TF superfamily that is involved in the lipid biosynthesis pathway. In covered barley, lipids on the surface of caryopses act as a glue for their tight adhesion with hulls. Separation of hulls in naked barley is due to the absence of surface lipids on caryopses. A natural deletion event of Nud was found to be the determinant of naked caryopsis and had been proposed as the monophyletic origin of domesticated naked barley. In the present study, we re-sequenced the nud locus in 162 barleys, comprising 79 covered and 83 naked barleys varieties. Besides the normal deletion mutation of Nud contributing to naked caryopsis, we found a novel allele of Nud, designated as nud1.g, distinctly in three naked barleys collected from Tibet. nud1.g contains a non-synonymous SNP T643A when compared with the functional Nud gene. Genetic analysis indicated that the SNP T643A of nud1.g co-segregates with the naked phenotype. The nud1.g gene was expressed normally in the three naked barleys. Furthermore, in silico prediction of functionally conserved sites and 3D structures showed that the amino acid substitution (valine to aspartate) caused by SNP T643A may lead to a dramatic structural alteration of NUD that may result in loss of function. This study provides evidence of a new origin of the naked phenotype of domesticated barley in Tibet.

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“…RNA quantity and quality check, library construction, and sequencing were performed as described by Dai et al (2014) and Wang et al (2016). The TruSeq RNA sample preparation kit (Illumina) was used to construct the library following the manufacturer's instructions.…”

Section: Rna-seqmentioning

confidence: 99%

Evolutionary Conservation of ABA Signaling for Stomatal Closure

et al. 2017

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Abscisic acid (ABA)-driven stomatal regulation reportedly evolved after the divergence of ferns, during the early evolution of seed plants approximately 360 million years ago. This hypothesis is based on the observation that the stomata of certain fern species are unresponsive to ABA, but exhibit passive hydraulic control. However, ABA-induced stomatal closure was detected in some mosses and lycophytes. Here, we observed that a number of ABA signaling and membrane transporter protein families diversified over the evolutionary history of land plants. The aquatic ferns Azolla filiculoides and Salvinia cucullata have representatives of 23 families of proteins orthologous to those of Arabidopsis (Arabidopsis thaliana) and all other land plant species studied. Phylogenetic analysis of the key ABA signaling proteins indicates an evolutionarily conserved stomatal response to ABA. Moreover, comparative transcriptomic analysis has identified a suite of ABAresponsive genes that differentially expressed in a terrestrial fern species, Polystichum proliferum. These genes encode proteins associated with ABA biosynthesis, transport, reception, transcription, signaling, and ion and sugar transport, which fit the general ABA signaling pathway constructed from Arabidopsis and Hordeum vulgare. The retention of these key ABA-responsive genes could have had a profound effect on the adaptation of ferns to dry conditions. Furthermore, stomatal assays have shown the primary evidence for ABA-induced closure of stomata in two terrestrial fern species P. proliferum and Nephrolepis exaltata. In summary, we report, to our knowledge, new molecular and physiological evidence for the presence of active stomatal control in ferns.

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Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

Cited by 74 publications

References 54 publications

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

A Single Nucleotide Polymorphism of Nud Converts the Caryopsis Type of Barley (Hordeum Vulgare L.)

Evolutionary Conservation of ABA Signaling for Stomatal Closure

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